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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattatacagcttgtaatacactgttcagcttttgttatttctcttatatgatacacactgatcatgaggacatgacacttgtaactcactggtattgtaaactatgcag

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G329306_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g11320.2 (Oryza sativa), 5'ss of exon 3
AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattatacagcttgtaataca-ctgttcagcttttgttatttctcttatatgatacacactgatcatgaggacatgacacttgtaactcactggtattgtaaactatgcag
|||||||| |||||||||||||| ||||||||||||||||| ||||| ||||||||  ||||||||||||||||||| ||||||||||| || |||||| |  |  | |||| |||||||   |||||| ||||| | | ||||| || ||||||||| |  || | |||    ||||  |||  |   |            
AAACAGGATTACAAGGCAGCTCTGAGAAAGTACAGGAAAGCACTGCGTTACTTGGACGTTTGCTGGGAGAAAGAAGATATAGATGAAGgcaa-ttatactgtct-cactacaactgttcaatgtttgttgtttctgtcacatgatgcatactgatcataaacacgtcaca----taac--acttatgcag------------

upper sequence: GRMZM2G329306_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0063g01030.t01 (Vitis vinifera), 5'ss of exon 3
AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattatacagcttgtaatacactgttcagcttttgttatttctcttatatgatacacactgatcatgag---gacatgac--acttgtaactc--actggtattgtaaactatgcag
|| || ||||| ||    || ||||| || ||  |||| ||| | ||||| |||||| | |||||||||||||||| ||| |||||||||    ||  |   || |   | |  ||   | ||||| | |||||||    ||||||  ||| ||  ||     |   ||||  | ||||   |   | |  |       ||| |||||
AAGCAAGACTATAAAATGGCACTCAGGAAATATCGGAAGGCTTTACGCTATTTGGATATATGCTGGGAGAAAGAAGGGATTGATGAAGgtgtgctacgcgttttctgtcataacgt---gtttttggtttttctctctcgtgataccaactaattgtgcctctgctgtgactgatttgtggtttttatttttccctgtcactctgcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71329028|gb|DR801213.1|DR801213
EST:     GGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: GGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32823335|gb|CD963057.1|CD963057
EST:     GATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: GATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCGCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32794497|gb|CD946733.1|CD946733
EST:     GATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: GATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCTCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32865832|gb|CF005514.1|CF005514
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCNCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAG                         ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT
genomic: AGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 106

AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 115

AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 176

AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 192

AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattata ... aactatgcagATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACAGGACTACAAGGCAGCTCTCAGAAAGTACAGGAAAGCTCTGCGCTACTTGGATCTTTGCTGGGAGAAAGAAGAGATAGATGAAGgtaaattatacagcttgtaatacactgttcagcttttgttatttctcttatatgatacacactgatcatgaggacatgacacttgtaactcactggtattgtaaactatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA